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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Test
Starch metabolism is a key process in plants and other organisms. It is an important in the storage of starch and utilization for other processes in the living cycles of plants. Starch is a stored carbohy-drate in plants which can later be used in carbohy-drate metabolism which plays an essential role in generating energy for the plant when there isn’t light available. Rather, starch is stored up until the night time when light isn’t available and continues creating energy for itself when photosynthesis cannot be done.
There are several enzymes associated with starch metabolism, the focus will be β-amylase (BAM) in the regulation process. β-amylase has an important role in degradation of starches within the plant. This study will focus on Arabidopsis tha-liana and the Arabidopsis plants generally have nine genes encoding for different types of β-amylases. Of the nine types, there is little infor-mation available for BAM6 or 7. While several of the BAM have confirmed catalytic activity within the plant, there is not enough data available for activity of BAM6 and 7, so structural analysis of both enzymes will be conducted using bioinformat-ics programs in order to predict functional similar-ities to other known BAM proteins.
Another featured studied with BAM proteins are the post-translational regulators of certain BAM types. Different post-translational regulators can change a variety of features of the protein, inhibi-tion, or protein interaction and more. The study will focus on glutathione (GSH), which is partly known to have some post-translational modifica-tions on a few of the known BAM proteins. The analysis of GSH modification of both BAM6 and BAM7 will be tested.
The structural similarities of BAM6 and BAM7 will be compared to each other as well as known BAM proteins in order to predict active or inactive functionality of the protein. The following proce-dures will follow a series of tests to determine the post-translational modifications of GSH on BAM. To validate the computational program experiments on BAM6 and 7, they will be followed up by an x-ray crystallography and Förster resonance energy transfer experiment to validate findings from the relevant computational data.
JPRED4
To determine the secondary structure of the pro-tein sequence of BAM6 and BAM7, JPRED4 was utilized. The webserver requires a single protein sequence and uses known homologs to output sec-ondary structure information on the sequence. The program utilizes an algorithm called Jnet to make secondary structure predictions of 82% or greater accuracy. JPRED4 will provide basic knowledge on the functional regions of both BAM proteins.
SwissModel
Enzyme that is part of starch breakdown - regu-lator
Sequence for Arabidopsis thaliana (β-AM-6 and BAM-7), however is found in many species includ-ing humans
β-AM has ~9 different forms in Ara. Some forms are active, some are inactive
Starch Metabolic pathways, starch is the most common carbohydrate found in plants. β-AM a part of starch degradation pathway in Ara (essential).
References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
